diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 220 |
1 files changed, 136 insertions, 84 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c7bf03bcbc..d404ff839c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1482,7 +1482,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.7.9") + (version "0.8.1") (source (origin (method url-fetch) (uri (string-append @@ -1491,33 +1491,18 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15")) - (snippet '(begin - (delete-file "bin/diamond") - #t)))) - (build-system gnu-build-system) + "1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc")))) + (build-system cmake-build-system) (arguments - '(#:tests? #f ;no "check" target + '(#:tests? #f ; no "check" target #:phases (modify-phases %standard-phases - (add-after 'unpack 'enter-source-dir - (lambda _ - (chdir "src") - #t)) - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) - (copy-file "../bin/diamond" - (string-append bin "/diamond")) - #t)))))) - (native-inputs - `(("bc" ,bc))) + (add-after 'unpack 'remove-native-compilation + (lambda _ + (substitute* "CMakeLists.txt" (("-march=native") "")) + #t))))) (inputs - `(("boost" ,boost) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (home-page "https://github.com/bbuchfink/diamond") (synopsis "Accelerated BLAST compatible local sequence aligner") (description @@ -2094,7 +2079,7 @@ particular, reads spanning multiple exons.") (source (origin (method url-fetch) (uri (string-append - "http://selab.janelia.org/software/hmmer" + "http://eddylab.org/software/hmmer" (version-prefix version 1) "/" version "/hmmer-" version ".tar.gz")) (sha256 @@ -2102,7 +2087,7 @@ particular, reads spanning multiple exons.") "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) - (home-page "http://hmmer.janelia.org") + (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description "HMMER is used for searching sequence databases for homologs of protein @@ -3570,7 +3555,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (define-public sortmerna (package (name "sortmerna") - (version "2.1") + (version "2.1b") (source (origin (method url-fetch) @@ -3580,7 +3565,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4")))) + "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) (build-system gnu-build-system) (outputs '("out" ;for binaries "db")) ;for sequence databases @@ -3600,6 +3585,8 @@ of these reads to align data quickly through a hash-based indexing scheme.") (install-file file share)) (find-files "rRNA_databases" ".*fasta")) #t)))))) + (inputs + `(("zlib" ,zlib))) (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") (synopsis "Biological sequence analysis tool for NGS reads") (description @@ -3831,7 +3818,7 @@ data in the form of VCF files.") (define-public vsearch (package (name "vsearch") - (version "1.10.0") + (version "1.11.1") (source (origin (method url-fetch) @@ -3841,7 +3828,7 @@ data in the form of VCF files.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5")) + "1pdvm3znjgq3zryy240yj9gc0bf1z31k6vf9jxrxgdgkvzgw85c7")) (modules '((guix build utils))) (snippet '(begin @@ -4018,13 +4005,13 @@ barplots or heatmaps.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.16.1") + (version "0.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0f16ryy5f012hvksrwlmm33bcl7lw97i2jvhbnwfwl03j4w7nhc1")))) + "1jjp48vbph09w5bmc7368gjjywsa1lmzfybpiwlypr60b51vlkp6")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -4038,13 +4025,13 @@ packages.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1c1px4rbr36xx929hp59k7ca9k5ab66qmn8k63fk13278ncm6h66")))) + "0vwv2mndfjpcjp4sybg75abc7xnx8zyw8zjk717k6xh8c33ymcip")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) @@ -4060,13 +4047,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.8.11") + (version "0.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "12iibcs63m9iy7f45wgjcqsna2dnqwckphk682389grshz0g4x66")))) + "1mi6lf6pnb9l657igy0vj4yz03yawbr2jhk22l757fzbjc7n9q3b")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -4087,13 +4074,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.4.8") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0hi5k1j5jm4xrg1l506g279qw1xkvp1gg1zgsjzpbng4vx4k4iyl")))) + "0dz7z0pk8hq79mcgylw920999s08h6j8xrl31rdxhssmi7l8v6vy")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -4116,13 +4103,13 @@ possible.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.6.3") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1ggp005n2rlkad00ilzn95y4rd484yr1chdhnd6fwg45rbi94d63")))) + "0k4s6z5qj53zkfnyrmcbn3l2nzgm56bhv58rv321j22qa56cpz7d")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -4142,13 +4129,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.16.4") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1z42j3p9b8h725inq8n0230llsdbav3gwcxy1nliypzfkxbzahsb")))) + "1jdpdnp7l81xfprba2ykfnj6i64fd84vxaax0wvrz6qahxvnjzyw")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -4174,13 +4161,13 @@ coding changes and predict coding outcomes.") (define-public r-xvector (package (name "r-xvector") - (version "0.10.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0havwyr6xqk7w0rmbwfj9jq1djz7wzdz7w39adhklwzwz9l4ih3a")))) + "0c9cqjcxxks3an4wiq167h2grxlfyazajn7bmxhbk42zifp8vmqp")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -4210,13 +4197,13 @@ coding changes and predict coding outcomes.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.22.4") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "02df5683nrpn9d10ws8jz9b55nr9055hh882xp2i154xdddir0k0")))) + "1iyzg1npl3rnnslwq3h759vf0xhshnn5v801rnlj6bnxzhn9yaqh")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -4237,13 +4224,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1qasjpq3kw8h7qw8cin3bjvv1256hqr1mm24fq3v0ymxzlb66szi")))) + "0q4icv9n5rc2qfkv6k1wjhmfcpzcyr8f45m2z3xharbdv912kl1i")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -4259,13 +4246,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.32.3") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1v6x62hgys5827yg2xayjrd9xawbayzm6wy0q4vxh1s6yxc9bklj")))) + "0nw6c23098gkjlwlrra4rh1m65azczb31qr01pq81cn5gya1zkr4")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -4286,13 +4273,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1s709055abj2gd35g6nnk5d2ai5ii09iir270l2xika6pi62gj3f")))) + "1g0w6an9hkflgyhvq6pmrs92s93qarv23v636b9a4bz771wjvm5v")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -4316,13 +4303,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.4.3") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1f5mndx66vampcsq0n66afg6x851crl0h3nyv2nyp9bsgzj9cdzq")))) + "0ki5xvb3cwjmlsx81gr8ylk1qy3imlj2dd04mzpvl28x42ay4dqj")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -4340,13 +4327,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.38.4") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0cjd7i4bdwabzb02gm753aji5xaihkj5ak8nb0d32cclxbj0hp33")))) + "03gyhiz14xy51nzg0glihk1rv19pq4p1aa3y5g23bzcshs67ggj9")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -4366,13 +4353,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1yc3nzzms3igjwr4l9yd3wdac95glcs08b4cfp7disyly0wcskjd")))) + "0w0drs8cpk8nlazq64ag7nm1w5jd1m8riialivm01hz5zcra7scb")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -4410,13 +4397,13 @@ files.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.0.2") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1gpmh1mi70m5k5qnyjs1h0qn8ajrzalzic7k3762xchxsmmdvxn4")))) + "1c81acgw3a0ha5fgapfh9xq8yhryqqf8k259n2dz0mgz1k2d9klg")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -4439,13 +4426,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "02b9j1pfd39bkvb623k5k0ziq9rpw093hifqw65vb954dwj29jhd")))) + "1y4qgqxq8dax9swgl59m6i7ggjpqrjllgx87b9vwls3z0nf1i6xj")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -4472,13 +4459,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.30.4") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0knjnwywh9k726mq28s3sy013zhw6d6nfa8hfw670720nq18i2p0")))) + "0nrwk1g8b1ymvbgnqniimbvwfq13r01va9rx3b03xj4hpywzy5nv")))) (build-system r-build-system) (arguments `(#:phases @@ -4517,13 +4504,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.22.13") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0n3rkj66la6wizgcsf2rmwcsyfxz9kv5zak337lmk1raqfnancz4")))) + "0ga5a7w8jnnq2k0kc07mshl6cggmbhzh42pzvhnilgl4x3kpbysl")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -4582,13 +4569,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-graph (package (name "r-graph") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "16w75rji3kv24gfv44w66y1a2y75ax26rl470y3ypna0ndc3rrcd")))) + "0ys5s19m5r30rlr0fnx2h0z2qw7n2xrad4l2yfb1bbrk8dwyf4pi")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -4601,13 +4588,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "029j9nb39b8l9xlzsp83pmjr8ap247aia387yzaa1yyw8klapdaf")))) + "1p4vsl32qhjw15yv9ym01ni63gjg73jaghlf17wc4zfn3iaz2zar")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -4616,6 +4603,7 @@ information about the latest version of the Gene Ontologies.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-go-db" ,r-go-db) + ("r-matrixstats" ,r-matrixstats) ("r-graph" ,r-graph) ("r-sparsem" ,r-sparsem))) (home-page "http://bioconductor.org/packages/topGO") @@ -4631,13 +4619,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "130w0m6q8kkca7gyz1aqj5jjhalwvwi6rk2yvbjrnj4gpnncyrd2")))) + "08g3w47ysbmgj4hclb0x2wsn7pi9cnm3xkkfk4shgrka2g23qz44")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -4661,13 +4649,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0y4x5jk7gsf4xn56jrkdcdnxpcfll4h6ivncd7n4snmzixldvmvw")))) + "0v9ibgv8kp8il52miz7b7z65mv6irqxylx6lfzkxgvxd970dgrz0")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -4681,13 +4669,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0p9zj6bic7sa0hb2bjm988kkk5n9r1kvlbqkzvy702f642n0j53i")))) + "1dj9hfnbdj11yjxwd8jmxrdkj7n6gmaaj6244g2psgarhjcp4wfb")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -4707,13 +4695,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.2.2") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0kvzwc21zsh2c8d34yn935ncn38bfkpzmknycd8h7b0521x20mi9")))) + "017hxh3yhizlsswd2vw8504arkckrcgq5zraiw67lldq9wzs5qzg")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -4854,14 +4842,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "0kn1a1nf2j4v9c09vjkz9bmxlln7yhg87bnyrdsxy1m55x56rn5k")))) + "01jddx62nhi3r7czbh9hxy0wwpazbc9ax1fgagfxl6p4kx9xz9rb")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "http://bioconductor.org/packages/seqLogo") @@ -5001,14 +4989,14 @@ Biostrings objects.") (define-public r-motifrg (package (name "r-motifrg") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn")))) + "1ds22paqc0923y6z1fy0arw0wxvvmglfvfgarhywv1qywhq68mbq")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -5053,13 +5041,13 @@ two-dimensional genome scans.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "01wc26ndg4jsn1wyrl6zzq636gxaip5fci0xapym4lh9wryc4wnw")))) + "0m8l7zpx1l3qsk73k3ibkxxzzff938x3qhnwki1ymf3cnsg8cb36")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -5069,6 +5057,70 @@ two-dimensional genome scans.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public piranha + (package + (name "piranha") + (version "1.1.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/smithlabcode/piranha" + "/archive/svn/tags/piranha-" + version ".tar.gz")) + (sha256 + (base32 + "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'copy-smithlab-cpp + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "src/smithlab_cpp") + (for-each (lambda (file) + (install-file file "./src/smithlab_cpp/")) + (find-files (assoc-ref inputs "smithlab-cpp"))) + #t)) + (add-after 'install 'install-to-store + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*"))) + #t))) + #:configure-flags + (list (string-append "--with-bam_tools_headers=" + (assoc-ref %build-inputs "bamtools") "/include/bamtools") + (string-append "--with-bam_tools_library=" + (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) + (inputs + `(("bamtools" ,bamtools) + ("samtools" ,samtools-0.1) + ("gsl" ,gsl) + ("smithlab-cpp" + ,(let ((commit "3723e2d")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit commit))) + (file-name (string-append "smithlab_cpp-" commit "-checkout")) + (sha256 + (base32 + "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) + (native-inputs + `(("python" ,python-2))) + (home-page "https://github.com/smithlabcode/piranha") + (synopsis "Peak-caller for CLIP-seq and RIP-seq data") + (description + "Piranha is a peak-caller for genomic data produced by CLIP-seq and +RIP-seq experiments. It takes input in BED or BAM format and identifies +regions of statistically significant read enrichment. Additional covariates +may optionally be provided to further inform the peak-calling process.") + (license license:gpl3+))) + (define-public pepr (package (name "pepr") |